Julian Rowe Dupuis

Julian Rowe Dupuis
University of Kentucky | UKY · Department of Entomology

PhD

About

46
Publications
10,297
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989
Citations

Publications

Publications (46)
Article
Species that are dispersed across oceanic islands can have strong population structure due to genetic isolation, which makes it difficult to determine realistic and meaningful species boundaries. This becomes especially problematic when pest species are involved, and can result in undetected new invasions. The mango fruit fly, Bactrocera frauenfeld...
Article
Divergence times underpin diverse evolutionary hypotheses, but conflicting age estimates across studies diminish the validity of such hypotheses. These conflicts have continued to grow as large genomics datasets become commonplace and analytical approaches proliferate. To provide more stable temporal intervals, age estimations should be interpreted...
Article
Full-text available
The swede midge, Contarinia nasturtii, is a cecidomyiid fly that feeds specifically on plants within the Brassicaceae. Plants in this family employ a glucosinolate-myrosinase defense system, which can be highly toxic to non-specialist feeders. Feeding by C. nasturtii larvae induces gall formation, which can cause substantial yield losses thus makin...
Preprint
Full-text available
The utility of a universal DNA ‘barcode’ fragment of 658 base pairs of the Cytochrome C Oxidase I (COI) gene for the recognition of all animal species has been a widely debated topic on theoretical and practical levels. Regardless of its challenges, large amounts of COI sequence data have been produced in the last two decades. To optimally use the...
Conference Paper
Full-text available
Bees are the most important pollinators in both managed and natural ecosystems, and yet concerns about bee declines are growing. Unfortunately, only a fraction of the 20,000 known bee species has adequate data to assess the status of species and susceptibility of populations to decline. The iDigBees Thematic Collections Network (TCN), comprised of...
Article
Full-text available
Population genomics is a useful tool to support integrated pest management as it can elucidate population dynamics, demography, and histories of invasion. Here, we use a restriction site-associated DNA sequencing approach combined with whole-genome amplification (WGA) to assess genomic population structure of a newly described pest of canola, the d...
Article
Allochronic isolation can be a strong mechanism for reproductive isolation and speciation. However, imperfect allochrony and the expression of phenological plasticity can erode temporal barriers to gene flow and result in hybridization between divergent lineages. Here, we combine behavioural ecology and genomics to investigate this scenario in two...
Article
Previous work in landscape genetics suggests that geographic isolation is of greater importance to genetic divergence than variation in environmental conditions. This is intuitive when configurations of suitable habitat are the dominant factor limiting dispersal and gene flow, but has not been thoroughly examined for habitat specialists with strong...
Article
Genomics has revolutionized our understanding of hybridization and introgression, but most of the early evidence for these processes came from studies of mitochondrial introgression. To expand these evolutionary insights from mitochondrial patterns, we evaluate phylogenetic discordance across the nuclear genomes of a hybridizing system, the Papilio...
Article
• Rare, threatened species often suffer from habitat fragmentation, which leads to smaller populations vulnerable to negative impacts including inbreeding depression and collapse of metapopulation dynamics. Therefore, understanding the population structure and relationships of each population of a threatened species is critical for prioritising hab...
Article
Full-text available
There is growing evidence for the decline of cryptic species across the planet as a result of human activities. Accurate data regarding patterns of poorly known or hard-to-find species diversity is essential for the recognition and conservation of threatened species and ecosystems. Casey’s June beetle Dinacoma caseyi is a federally listed endangere...
Article
Full-text available
In the context of evolutionary theory, invasion biology provides a fantastic enigma: how does a species with limited standing genetic variation survive and adapt to a novel environment? Reduced genetic diversity is typically associated with low fitness and evolutionary potential, yet some introduced species have proven to be successful invaders des...
Article
Full-text available
Phylogeographic patterns in phytophagous organisms are often contextualized in light of geographic isolation and ecological (host, habitat) specialization. However, assessing the relative impact of these phenomena is not straightforward, even in areas where phylogeography is well-studied, such as the California Floristic Province. Here, we use geno...
Article
Full-text available
Populations delineated based on genetic data are commonly used for wildlife conservation and management. Many studies use the program structure, combined with the ΔK method to identify the most probable number of populations (K). We recently found K = 2 was identified more often when studies used ΔK compared to studies that did not. We suggested tw...
Article
A new species, Contarinia brassicola Sinclair (Diptera: Cecidomyiidae), which induces flower galls on canola (Brassica napus Linnaeus and Brassica rapa Linnaeus (Brassicaceae)), is described from Saskatchewan and Alberta, Canada. Larvae develop in the flowers of canola, which causes swelling and prevents opening, pod formation, and seed set. Mature...
Article
Full-text available
Compared to traditionally used plastid or ribosomal markers, nuclear gene markers provide many advantages for molecular systematics of plants, and high-throughput sequencing technologies are making large nuclear datasets available at an unprecedented rate. We used targeted amplicon sequencing of 44 nuclear genes to construct a time-calibrated phylo...
Article
Compared to traditionally used plastid or ribosomal markers, nuclear gene markers provide many advantages for molecular systematics of plants, and high-throughput sequencing technologies are making large nuclear datasets available at an unprecedented rate. We used targeted amplicon sequencing of 44 nuclear genes to construct a time-calibrated phylo...
Article
Full-text available
Recurrently invading pests provide unique challenges for pest management, but also present opportunities to utilize genomics to understand invasion dynamics and inform regulatory management through pathway analysis. In the southern United States, the Mexican fruit fly Anastrepha ludens is such a pest, and its incursions into Texas and California re...
Article
Butterflies have played a pivotal role in our understanding of animal movement, but little is known about landscape-scale movement in highly vagile species with large ranges and open population structure. We investigate the effect of environment and landscape on both inter- and intraspecific genetic differentiation and population structure in the P...
Article
Full-text available
Conservation geneticists have argued that evolutionarily significant units (ESUs) must be both genetically distinct and adaptively significant to be recognized for conservation protection. High-throughput DNA approaches can greatly increase the power to identify genetic distinctiveness, even if inferring adaptive significance remains a challenge. H...
Article
Local adaptation can be a fundamental component of speciation, but its dynamics in relation to gene flow are not necessarily straightforward. Herbivorous taxa with localized host plant or habitat specialization across their geographic range are ideal models for investigating the patterns and constraints of local adaptation and its impact on diversi...
Article
Species delimitation and identification are integral to virtually all biological disciplines, but are far from straightforward tasks. Taxonomy has recently focused on integrative approaches that consider multiple types of data to resolve species boundaries, yet methodologies to that end are still being developed. Here, we assess species limits in a...
Article
1.Sampling markers throughout a genome with restriction enzymes emerged in the 2000s as reduced representation shotgun sequencing (RRS). Rapid advances in sequencing technology have since spurred modifications of RRS, giving rise to many derivatives with unique names, such as restriction site‐associated DNA sequencing (RADseq). But naming conventio...
Article
New World screwworm (NWS), Cochliomyia hominivorax (Coquerel 1858) (Diptera: Calliphoridae), is a myiasis-causing fly that can be a serious threat to the health of livestock, wildlife, and humans. Its progressive eradication from the southern United States, Mexico, and Central America from the 1950s to 2000s is an excellent example of successful pe...
Article
Full-text available
Population genetics is a powerful tool for invasion biology and pest management, and useful for a range of questions from tracing invasion pathways to informing management decisions with inference of population demographics. Genomics greatly increases the resolution of population-scale analyses, yet outside of model species with extensive genomic r...
Article
High‐throughput sequencing has fundamentally changed how molecular phylogenetic datasets are assembled, and phylogenomic datasets commonly contain 50‐100‐fold more loci than those generated using traditional Sanger‐based approaches. Here, we demonstrate a new approach for building phylogenomic datasets using single tube, highly multiplexed amplicon...
Preprint
Full-text available
Sampling markers throughout a genome with restriction enzymes emerged in the 2000s as reduced representation shotgun sequencing (RRS). Rapid advances in sequencing technology have since spurred modifications of RRS, giving rise to many derivatives with unique names, such as RADseq. But naming conventions have often been more creative than consisten...
Article
Swallowtail butterflies (Lepidoptera: Papilionidae) have been instrumental in understanding many foundational concepts in biology; despite this, a resolved and robust phylogeny of the group has been a major impediment to elucidating patterns and processes of their ecological and evolutionary history. This study presents a mitogenomic, time-calibrat...
Article
Full-text available
The aim was to determine processes driving the latitudinal diversity gradient (LDG) in New World swallowtail butterfly diversity. We tested three mechanisms commonly invoked to explain the LDG: ecological opportunity, evolutionary rates and biogeographical history. New World and Eurasia. Oligocene–Present. New World swallowtail butterfly clade (Pap...
Preprint
Full-text available
High-throughput sequencing has fundamentally changed how molecular phylogenetic datasets are assembled, and phylogenomic datasets commonly contain 50-100-fold more loci than those generated using traditional Sanger-based approaches. However, many of the commonly used approaches for generating phylogenomic datasets are prohibitively expensive for mo...
Article
Full-text available
Characterizing genetic structure across geographic space is a fundamental challenge in population genetics. Multivariate statistical analyses are powerful tools for summarizing genetic variability, but geographic information and accompanying metadata is not always easily integrated into these methods in a user-friendly fashion. Here, we present a d...
Chapter
This chapter reviews the molecular dimensions of insect taxonomy by focusing on high-throughput sequencing and other genomic advances. It then focuses on three facets of the emerging relationship among taxonomy, systematics, and genomic methodology. The chapter addresses taxonomy conceptually, considering the four fundamental problems in taxonomic...
Article
Full-text available
High-throughput sequencing methods for genotyping genome-wide markers are being rapidly adopted for phylogenetics of non-model organisms in conservation and biodiversity studies. However, the reproducibility of SNP genotyping and degree of marker overlap or compatibility between datasets from different methodologies have not been tested in non-mode...
Article
Full-text available
Assessments of population genetic structure have become an increasing focus as they can provide valuable insight into patterns of migration and gene flow. STRUCTURE, the most highly cited of several clustering-based methods, was developed to provide robust estimates without the need for populations to be determined a priori. STRUCTURE introduces th...
Article
High throughput sequencing technologies have revolutionized the potential to reconcile incongruence between gene and species trees, and numerous approaches have been developed to take advantage of these advances. Genotyping-by-sequencing is becoming a regular tool for gathering phylogenetic data, yet comprehensive evaluations of phylogenetic method...
Article
Hybrid zones provide unique natural laboratories for studying mechanisms of evolution. But identification and classification of hybrid individuals (F1, F2, backcross, etc.) can be complicated by real population changes over time as well as by use of different marker types, both of which challenge documentation of hybrid dynamics. Here we use multip...
Article
Full-text available
Diapause that extends across multiple years is considered a bet-hedging strategy in insect species that are exposed to unfavorable environmental conditions. The dynamics of extended diapause in herbivores can be complicated when their parasitoids can also extend diapause, although our knowledge of these dynamics is based primarily on pest species....
Article
Full-text available
Hybridization between distinct populations or species is increasingly recognized as an important process for generating biodiversity. However, the interaction between hybridization and speciation is complex, and the diverse evolutionary outcomes of hybridization are difficult to differentiate. Here we characterize potential hybridization in a speci...
Article
Full-text available
The Mormon Metalmark (Apodemia mormo) species complex occurs as isolated and phenotypically variable colonies in dryland areas across western North America. Lange's Metalmark, A. m. langei, one of the 17 subspecies taxonomically recognized in the complex, is federally listed under the U.S. Endangered Species Act of 1973. Metalmark taxa have traditi...
Conference Paper
The reticulate nature of hybridization violates the basic assumption of tree-like evolution in phylogenetics. From an analytical perspective, differential introgression often creates incongruence between datasets, thus complicating the inference of species phylogenies from gene phylogenies. Despite these difficulties, hybrid systems offer unique op...
Article
Despite taxonomy's 250-year history, the past 20 years have borne witness to remarkable advances in technology and techniques, as well as debate. DNA barcoding has generated a substantial proportion of this debate, with its proposition that a single mitochondrial sequence will consistently identify and delimit species, replacing more evidence-rich...

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Project (1)
Archived project
A meta-analysis/review/opinion on the prevalence of delta K use and potential biases in reporting K=2.